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E. coli C-P lyase bound to PhnK/PhnL dual ABC dimer with AMPPNP and PhnK E171Q mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XB6
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.4647 f_angle_d 0.4808 f_chiral_restr 0.0457 f_plane_restr 0.0035 f_bond_d 0.0017
Sample E. coli C-P lyase bound to PhnK/PhnL dual ABC dimer with AMPPNP and PhnK E171Q mutation
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details Blotting for 6-9 seconds before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 59737 Reported Resolution (Å) 2.09 Resolution Method FSC 0.143 CUT-OFF Other Details reconstruction using cryoSPARC homogeneous refinement Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (4XB6) Refinement Space RECIPROCAL Refinement Protocol Refinement Target Overall B Value 28.8 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 62
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 1400 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 135000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 3.2 INITIAL EULER ASSIGNMENT cryoSPARC 3.2 FINAL EULER ASSIGNMENT cryoSPARC 3.2 CLASSIFICATION cryoSPARC 3.2 RECONSTRUCTION cryoSPARC 3.2 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1023261 Deep picker from cryoSPARC used